Variant chr11-45910171-TGGGACGCTGCCGGAGTCAGTTTTATTAGGGAAGAGGGGCTCCCTGCCCCACCCCTCCCCACACCCTCCTTCCGGGAGGTCTGTCAGCCCCAACTGTAGAAGTAGATTTTCTGCCAGGTGGGCAAGTAATCCATGAGCGGCCCTGCAGTGGGAGAGGGACACATCAGGGCAGGCCAGACCCCAATCTGCACTGTGGCGCCACATACAGCACCTCACCCCTGCGGCCCAGGAGCCAGCCCAGCTGGCTGTCTTGCCCTGCCCCCAGGAGGCAGCACTGCAGGGGACTCTGGCACCATTTACAAAGACCCTCAGGCCCAGAGAAGCTCAGCCAGGGTAGACACTGAGGGGCCTGAGTCAGGTCCAGTCACCCAACCCAAGCCCAGTGGGCCTCTGCTGAGGGAGGATCTCAGCAGCCCGGTGGACCCCTTCTCTGCCATTGAATCCCCCCAAGATGAGATGGTCCCGTATCGCTCCAGGATACTGTGACCAGAAAAAAGCTGGCAGCTGATGTGGTCCCCCCACCAGTGGACACCCTCCTTCCAGCCATCCCTGGCTCCTCAGGCCACCCTGGCCTATGCCCAGGGGCAGTCCCACCCAATCCTGACTTCCC-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5

The NM_004813.4(PEX16):c.952+118_*82del variant causes a splice acceptor, coding sequence, 3 prime UTR, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).

Frequency

Genomes: not found (cov: 33)

Consequence

PEX16
NM_004813.4 splice_acceptor, coding_sequence, 3_prime_UTR, intron

Scores

Not classified

Clinical Significance

Pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: 1.64

Variant links:

Genes affected

PEX16 (HGNC:8857): (peroxisomal biogenesis factor 16) The protein encoded by this gene is an integral peroxisomal membrane protein. An inactivating nonsense mutation localized to this gene was observed in a patient with Zellweger syndrome of the complementation group CGD/CG9. Expression of this gene product morphologically and biochemically restores the formation of new peroxisomes, suggesting a role in peroxisome organization and biogenesis. Alternative splicing has been observed for this gene and two variants have been described. [provided by RefSeq, Jul 2008]

PEX16 links:

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 11 ACMG points.

PVS1

Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease,

PM2

Very rare variant in population databases, with high coverage;

PP5

Variant 11-45910171-TGGGACGCTGCCGGAGTCAGTTTTATTAGGGAAGAGGGGCTCCCTGCCCCACCCCTCCCCACACCCTCCTTCCGGGAGGTCTGTCAGCCCCAACTGTAGAAGTAGATTTTCTGCCAGGTGGGCAAGTAATCCATGAGCGGCCCTGCAGTGGGAGAGGGACACATCAGGGCAGGCCAGACCCCAATCTGCACTGTGGCGCCACATACAGCACCTCACCCCTGCGGCCCAGGAGCCAGCCCAGCTGGCTGTCTTGCCCTGCCCCCAGGAGGCAGCACTGCAGGGGACTCTGGCACCATTTACAAAGACCCTCAGGCCCAGAGAAGCTCAGCCAGGGTAGACACTGAGGGGCCTGAGTCAGGTCCAGTCACCCAACCCAAGCCCAGTGGGCCTCTGCTGAGGGAGGATCTCAGCAGCCCGGTGGACCCCTTCTCTGCCATTGAATCCCCCCAAGATGAGATGGTCCCGTATCGCTCCAGGATACTGTGACCAGAAAAAAGCTGGCAGCTGATGTGGTCCCCCCACCAGTGGACACCCTCCTTCCAGCCATCCCTGGCTCCTCAGGCCACCCTGGCCTATGCCCAGGGGCAGTCCCACCCAATCCTGACTTCCC-T is Pathogenic according to our data. Variant chr11-45910171-TGGGACGCTGCCGGAGTCAGTTTTATTAGGGAAGAGGGGCTCCCTGCCCCACCCCTCCCCACACCCTCCTTCCGGGAGGTCTGTCAGCCCCAACTGTAGAAGTAGATTTTCTGCCAGGTGGGCAAGTAATCCATGAGCGGCCCTGCAGTGGGAGAGGGACACATCAGGGCAGGCCAGACCCCAATCTGCACTGTGGCGCCACATACAGCACCTCACCCCTGCGGCCCAGGAGCCAGCCCAGCTGGCTGTCTTGCCCTGCCCCCAGGAGGCAGCACTGCAGGGGACTCTGGCACCATTTACAAAGACCCTCAGGCCCAGAGAAGCTCAGCCAGGGTAGACACTGAGGGGCCTGAGTCAGGTCCAGTCACCCAACCCAAGCCCAGTGGGCCTCTGCTGAGGGAGGATCTCAGCAGCCCGGTGGACCCCTTCTCTGCCATTGAATCCCCCCAAGATGAGATGGTCCCGTATCGCTCCAGGATACTGTGACCAGAAAAAAGCTGGCAGCTGATGTGGTCCCCCCACCAGTGGACACCCTCCTTCCAGCCATCCCTGGCTCCTCAGGCCACCCTGGCCTATGCCCAGGGGCAGTCCCACCCAATCCTGACTTCCC-T is described in ClinVar as [Pathogenic]. Clinvar id is 30353.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PEX16	NM_004813.4 linkuse as main transcript	c.952+118_*82del		splice_acceptor_variant, coding_sequence_variant, 3_prime_UTR_variant, intron_variant	11/11	ENST00000378750.10	NP_004804.2

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PEX16	ENST00000378750.10 linkuse as main transcript	c.952+118_*82del	splice_acceptor_variant, coding_sequence_variant, 3_prime_UTR_variant, intron_variant	11/11	1	NM_004813.4	ENSP00000368024	P1	Q9Y5Y5-1
PEX16	ENST00000241041.7 linkuse as main transcript	c.952+118_958del	splice_acceptor_variant, coding_sequence_variant, intron_variant	11/11	1		ENSP00000241041		Q9Y5Y5-2
PEX16	ENST00000532681.5 linkuse as main transcript		splice_acceptor_variant, coding_sequence_variant, 3_prime_UTR_variant, intron_variant	11/11	3		ENSP00000434654
PEX16	ENST00000523721.2 linkuse as main transcript	n.182+118_323del	splice_acceptor_variant, non_coding_transcript_exon_variant, intron_variant	3/3	5

Frequencies

GnomAD3 genomes

Cov.:

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

Cov.:

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Peroxisome biogenesis disorder 8B

Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Sep 01, 2010

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.